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OPENSEQ.org
DNAN_DPO3B_SALTY-UMUC_SALTY HHBlits
Genes: A B A+B
Length: 366 422 761
Sequences: 7006 15934 2899
Seq/Len: 19.14 37.76 3.81
MirrorTree (Pazo et al. 2001) 0.14
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.01 0.03
20 0.00 0.01 0.10
100 0.00 0.02 0.54
∞ 0.01 0.07 3.68
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
216_V 75_E 0.72 0.37 0.00
286_S 190_R 0.68 0.32 0.00
10_L 206_L 0.67 0.31 0.00
35_L 253_F 0.67 0.30 0.00
195_V 225_T 0.65 0.28 0.00
116_F 69_C 0.65 0.28 0.00
33_L 49_I 0.64 0.27 0.00
39_D 174_R 0.64 0.27 0.00
290_L 309_A 0.64 0.27 0.00
123_Q 380_L 0.62 0.25 0.00
141_S 49_I 0.61 0.25 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
7080 3.81 DNAN_DPO3B_SALTY-UMUC_SALTY HHBlits Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6932 0.03 DNAN_DPO3B_SALTY-UMUC_SALTY HHBlits Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6891 0.1 DNAN_DPO3B_SALTY-UMUC_SALTY Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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